The next season Kinnear continued to defy the odds and Wimbledon finished 9th in the league. The achievements are made even more respectable considering the Dons had no home of their own and had a small transfer budget.

It was reported that Kinnear turned down the chance to replace Jack Charlton as manager of the Republic of Ireland national team in 1996. Kinnear then guided Wimbledon to semi-finals in both of the major domestic cup competitions in 1997 as well as finishing 8th in the Premier League. However, when Wimbledon were taken over by new Norwegian owners after the end of that season, it was widely reported that Kinnear would be axed as manager in favour of Norwegian coach Age Hareide, but the change of management never happened and Kinnear remained at the Wimbledon helm for a further two seasons.[16]

Kinnear continued in his role as Wimbledon until he suffered a heart attack before a league game against Sheffield Wednesday in March 1999. He stood down in June of that year and as was replaced at Wimbledon by Egil Olsen.[13][17] Wimbledon were relegated from the Premier League in the following season.

He could not save the club from relegation, despite purchasing striker Steve Howard for £50,000 on transfer deadline day. In the summer of 2001, Kinnear released the majority of the relegated squad, and brought in a number of his own men over the course of the season, including future captains Kevin Nicholls and Chris Coyne, along with winger Jean-Louis Valois. The team stormed to promotion under Kinnear's guidance, finishing runners-up to Plymouth Argyle in the Hatters' first promotion in 20 years.

The next season was disappointing for the Hatters, as they were expected to compete for promotion, but in the end they only managed a 9th place finish. In May 2003 the club was sold to a consortium, led by John Gurney,[21] and Kinnear and his assistant Mick Harford were then sacked,[21] in mysterious circumstances[22] which involved an employee of Northampton Town being the person who signed the letters which dismissed both Kinnear and Harford.

Kinnear was out of work until Nottingham Forest offered him the manager's job in February 2004,[23] taking over from Paul Hart.[23] Forest were in the bottom third of the league table when he took over, but he would have an immediate impact on the club.[24] Kinnear was able to get the club up to 14th position by the end of the 2003–04 season. The following season began with talk of promotion,[25] but would go badly for Forest and Kinnear, with just four wins from the first 23 games in the league that year. A 3–0 defeat to rivals Derby County at Pride Park,[26] signalled the end for Kinnear, with his resignation coming on 16 December 2004.[26][27] Nottingham Forest were 22nd in the Football League Championship table following Kinnear's departure, the club appointed Mick Harford to take over as interim manager. Forest would ultimately be relegated at the end of the season, after Gary Megson had been appointed as the full-time replacement to Kinnear.

Kinnear was without a club following his departure from Nottingham Forest for almost four years, though there were rumours about joining several clubs during this time including QPR.[28] On 26 September 2008, Kinnear was named as the interim manager of Premier League side Newcastle United until the end of October, following the resignation of Kevin Keegan.[29] This initial one-month period was extended for an additional month, keeping Kinnear at St. James' Park until the end of December.[30][31]

On 2 October 2008, after a controversial start to his tenure at Newcastle, he launched a verbal tirade at the Daily Mirror's journalist Simon Bird calling him a "cunt".[32][33] He swore 52 times in the interview with Bird and other members of the media. The club's press officer tried to order the assembled journalists not to publish any extracts from the tirade, but Kinnear himself gave the journalists permission to write up whatever they wanted from his remarks. Later in the interview, he announced that he would no longer deal with the national media while he was Newcastle manager, and that he would only speak to local newspapers from then on, with first team coach Chris Hughton handling all other interviews.

Kinnear's first two games in charge, against Everton and Manchester City, both ended as 2–2 draws. Kinnear's first win at Newcastle was against West Brom. Newcastle won the match 2–1, with the first goal coming from Joey Barton, who was making his first starting appearance for Newcastle since being released from prison during the summer.[34] He then followed this up with a surprise win against fifth placed Aston Villa to lift Newcastle off the foot of the table and out of the relegation zone. Two goals from Obafemi Martins secured the 2–0 victory.

On 31 October 2008, Kinnear stated that 22 November would be D–Day with regards to the sale of Newcastle United and his position as manager.[35] This turned out to be untrue, as Kinnear was confirmed as being in charge for another month after Newcastle's 0–0 draw with Chelsea.[36] On 28 November, Kinnear was named as the permanent manager of Newcastle until the end of the 2008–09 season.[37]

Kinnear continued his event filled season in charge by getting sent off on 6 December after a confrontation with referee Mike Riley during a 2–2 draw with Stoke City, having been up by two goals for most of the match.[38] After that disappointing draw with Stoke they followed with wins against Portsmouth and Tottenham Hotspur, which was Newcastle's fifth consecutive league victory against the North London team.[39]

Following a 5–1 defeat to Liverpool on 28 December, Kinnear re-affirmed his belief that the Newcastle squad lacked strength in depth – with the manager having fielded a makeshift side due to injuries and suspensions resulting from the 2–1 Boxing Day defeat to Wigan – and stated that he was looking to improve the side with transfers in the January window.[40] In January, Kinnear secured the signings of Peter Løvenkrands, Kevin Nolan and Ryan Taylor. The latter had been signed in a part exchanged deal with Charles N'Zogbia. N'Zogbia had frequently stated in the press, via his agent, that he wished to leave. The final straw came after Kinnear mispronounced N'Zogbia's name during an interview in which he called him 'insomnia'. N'Zogbia stated that he no longer wished to play for Newcastle as long as Kinnear was the manager.[41]Shay Given was also sold to Manchester City for £7m.[42]

On 7 February 2009, Kinnear was taken to hospital after feeling ill, hours before Newcastle's clash with West Brom. The club stated that it was just precautionary and that Chris Hughton would take charge of the team. Newcastle won 3–2, their first win since Christmas. It was later announced Kinnear would need a heart bypass operation[43] and that Alan Shearer would take over the managerial role for the remainder of the season. Joe Kinnear's contract officially expired at Newcastle on 30 May 2009.[44]

On 14 August on the 3 Legends radio show, it was announced that Kinnear would be re-appointed as the club's manager the following Monday, this after Kinnear had himself declared that Mike Ashley had approached him to return but that he was unable to do so immediately because of his medical condition. However, with Mike Ashley taking the club off the market and Chris Hughton securing an excellent start to the season for Newcastle, Kinnear did not return to St James' Park.

On 16 June 2013 in a series of telephone interviews Kinnear claimed he had been appointed as Director of Football for Newcastle United.[45] In a Talksport interview over the telephone on 17 June 2013, Kinnear claimed to have replaced someone called "Derek Lambesi" (sic) as the club's director of football, signed Dean Holdsworth at Wimbledon for £50,000 (actually £650,000), sold Robbie Earle (retired a year after Kinnear left), signed goalkeeper Tim Krul when he was previously manager (actually signed by Graeme Souness three years prior) and has been awarded the LMA Manager of the Year award three times despite only winning the award once, he also said he'd never been sacked in his life.[46][47] Kinnear claimed to have signed John Hartson on a free when he in fact paid £7.5 million for the striker. He also mispronounced the names of Yohan Cabaye, Hatem Ben Arfa, Shola Ameobi, and others in the Talksport interview.[48][49] The appointment, a three-year contract, was confirmed by Newcastle United on 18 June.[50] The confusion around Kinnear's appointment to the role was criticised by former club chairman Freddy Shepherd in an interview with BBC Sport.[51] Kinnear drew criticism when the 2013 summer transfer window closed with Kinnear failing to make a single permanent signing,[52] lone recruit Loic Remy having been signed on loan from QPR. This criticism intensified at the end of the 2014 winter transfer window with Kinnear failing again to make a permanent signing, this after the £20 million sale of midfielder Yohan Cabaye, with Luuk de Jong having been brought in on loan from Monchengladbach.[53]

On 3 February 2014, Kinnear resigned from his position of Director of Football at Newcastle United.[54][55]